teaguesterling/plinking_duck v0.9.0

on GitHub

Builds against DuckDB 2.0.0 as well as the pinned v1.5 line.

• A SIGSEGV in the logistic path. plink-ng's float kernels use aligned AVX loads (_mm256_load_ps), which fault on anything less than 32-byte alignment, and LogisticBuffers held its scratch in std::vector<float> — which guarantees only 16. Latent: it crashed on one DuckDB build and passed on another with identical source.
• Ploidy-aware plink_score and plink_missing on sex chromosomes. Haploid calls on chrY/chrMT now contribute one allele rather than two, and chrY excludes females and unknown-sex samples instead of mean-imputing a score for a chromosome they lack. plink_glm's chrX handling is documented rather than silently assumed — plink2 couples chrX with an injected sex covariate, which is a modelling decision rather than a bug fix.
• Signed LD and population-weighted LD, contributed by @sounkou-bioinfo, rebased onto current main with authorship preserved.
• Under-allocated Hessian scratch corrected to plink-ng's own floors (p * MAXV(p, 7) and p * MAXV(p, 3)).

4751 assertions; canary Build and Test both green against DuckDB main.